Hi-
Can you please clarify some points to your question:
1) What to3d command are you specifically using?
2) And what error/output message or behavior are you receiving?
3) You mention having 3D data; the previous case was specifically for 4D data, where one of the 3D spatial dimensions was "1". Is your case reconstructing a single volume (purely spatial dataset), or does it have a time axis? Basically, what is your specific input data?
4) I think Daniel's suggestion of including "-orient ..." information in the previous question in this thread is the thing to include to not get the pop-up/interactive session. Are you including that? (This response will be clarified by your answer to Q1.)
--pt